The time course of attentional alerting can be differentiated in two phases: a quick and automatic initial phasic alerting, and slower, more strategic tonic alerting. Recently, in a series of behavioral flanker task experiments, we have demonstrated that phasic and tonic alerting (induced by accessory cues with short and long SOA) have distinct effects on conflict resolution. Phasic alerting decreased the efficiency of conflict resolution both in time and accuracy of responses, whereas tonic alerting increased the accuracy of conflict resolution, but at a cost in speed of processing the conflict (Asanowicz & Marzecová, 2017, Acta Psychol). In the present study, we recorded event-related EEG potentials to examine the brain mechanisms of these effects. Thirty-two participants performed an arrow flanker task with auditory alerting cues preceding target arrows with short (100 ms) or long (800 ms) SOA. We utilized N2pc components as indices of stimulus selection, LRP components as indices of response conflict, and frontal N2/P2 and P3b components as indices of control processes. Both behavioral and ERP results showed differential effects of phasic and tonic alerting on conflict resolution. The ERP results revealed that the alerting effects had different temporal dynamics, and affected stimulus processing and response conflict resolution at different stages of these processes. Presumably, as it has been previously suggested, phasic alerting inhibits executive control and redirects the allocation of attentional resources to facilitate responding to external events, whereas tonic alerting allows to endogenously increase readiness to process expected stimuli and thereby better response preparation.